LOCUS       CP125047                5874 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-C10 plasmid pKFS-C10_3, complete
            sequence.
ACCESSION   CP125047
VERSION     CP125047.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598743
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5874)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Genomic surveillance of antimicrobial-resistant Escherichia coli in
            fecal sludge and sewage in Uganda
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5874)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAY-2023) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. v2.9.1-b1780
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/09/2023 16:59:26
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,998
            CDSs (total)                      :: 4,876
            Genes (coding)                    :: 4,619
            CDSs (with protein)               :: 4,619
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 86 of 257
            Pseudo Genes (incomplete)         :: 177 of 257
            Pseudo Genes (internal stop)      :: 48 of 257
            Pseudo Genes (multiple problems)  :: 52 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..5874
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-C10"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-C10_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(1064..1930)
                     /locus_tag="QL142_24875"
     CDS             complement(1064..1930)
                     /locus_tag="QL142_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0005215 - transporter activity [Evidence IEA];
                     GO_process: GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WHJ45399.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(1932..2984)
                     /locus_tag="QL142_24880"
     CDS             complement(1932..2984)
                     /locus_tag="QL142_24880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ45400.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGNGGYSHPEGISTTWHSESKLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIDNSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGVPVDDASMFFNSFQPRKFE
                     NNPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(3704..3937)
                     /locus_tag="QL142_24885"
     CDS             complement(3704..3937)
                     /locus_tag="QL142_24885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WHJ45396.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3944..4474)
                     /locus_tag="QL142_24890"
     CDS             complement(3944..4474)
                     /locus_tag="QL142_24890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WHJ45397.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(4512..4943)
                     /locus_tag="QL142_24895"
                     /pseudo=""
     CDS             complement(4512..4943)
                     /locus_tag="QL142_24895"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(5152..5475)
                     /locus_tag="QL142_24900"
     CDS             complement(5152..5475)
                     /locus_tag="QL142_24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHJ45401.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAAWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALIAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5541..5732
                     /locus_tag="QL142_24905"
     CDS             5541..5732
                     /locus_tag="QL142_24905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WHJ45398.1"
                     /translation="MTKQEKTALNMVRFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(491..678)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3601..5162)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.232"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atactggctt aatcattcgg catcagtgcg gattgtatga aaagtgcgcc atgtcgggtg
       61 tgaaatgccg cacagatgcg taaggagaaa atgccagttc aggcgctctt ccgcttcctc
      121 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggactctc ctttctcaaa
      181 aacgctaacc ctgttatcca cagaacccgg ggataaacca ggaaagaaca tgtgcgcaaa
      241 aaacgaaacc ccggaaaagg ccgcgccgga ggcgcttttt ccataggctc cgcccccctg
      301 acggacttca caaaacagac actttttcgg tgcatctgtg ggagccttgc ggctcaacca
      361 tgaaatccgc cagcggtggc gaaacccgac gtggcttaaa gatcatcacc gtttccggtg
      421 aatcgctccc tcctgcgccc ccacgttccc gccatatcga ttaccggata ccttttccgc
      481 ctttctccct tacgggacac gtggcgcttt ctcatagctc acgtcttctg gtatctcggg
      541 gcgacttagg cagttcgctc cgggctgggc tgtatgcagg aaccccccgt tcagcccgac
      601 tgctgcgcct tctccggtaa ctgttctctt gggtccaacc cggaaaagac accacaaagc
      661 gccactggca gcagccattg gtaaaagtca tgtgcgagat atttagagag tacttgaagt
      721 ggctgccgga gtgcggctac actagaagaa caattttggt gactcgtctc gcataagaca
      781 gttacctggt taagcagtct gcaagctgac ttaaccttcg atcaaaccgc cctgcaaggc
      841 ggttttttcg tttacaggca gcagattacg cgcagaaaaa aaggatctca agaggatcct
      901 ttgatctttt tgttacaaac gtctctattt gactcccctg agagcgtttt agcgcgcctc
      961 tgccccccct tggttacatt ccgacaccag aaacgctccc gttttttacg tgcatttggc
     1021 acggtatcga tggaggccgg ggggggcaat cctgaacaga atgttactcc tctgagtatt
     1081 ttctgttaag aaaatataca cttagcacag ttacaataaa tcctaccccc tgtaagaatg
     1141 tgaattgttc atccaaaaac aaccatgaca aaaataatgc aactagcgga ataaagtaca
     1201 acattatccc tgccaaatga actgggagcc aacgcaagga gttcaagtaa aaacaaaaag
     1261 ctaaaaaata ttgtaatatt ccagatgaaa aaacaataat cacggattcc aacggaagat
     1321 aaattgagga tttagatata aaaataaaga gcgatgacag tataagggag aatgtcaact
     1381 gtccgctcaa taatgtgata ggctcaaacg atttaataag gcgagacgat ataacaacat
     1441 aaaatgctgc cgataacaca ccggcaacaa caagacaata tccaacaata ttattcgatc
     1501 cattactgat gtctggcaag gctaccaaaa tactgccaac aattgcacct ataaggaaca
     1561 atataaaata ttgcggggaa ttaattttaa ctgagcaaat aagaacagac aacaccaata
     1621 taaacactga ttcaagtgaa aaaataattg atgcgcttcc tgctgaaata aaataaagtc
     1681 cgtagagtgt aaaagtatac gctaagaatg gttcaaaaac gcctgtcgca taagcaagta
     1741 tcgcttttga gtttaatggg agtttttttc tttttataaa aagaactatc caagatagta
     1801 ttactgcact acaaatctgc cagaaaaaca cccctccggc atctagttct tcaactcctt
     1861 ttttgctcat tacgatagct gccccccatg agaacgctgc taaaaaagca aaaagcattc
     1921 ctttaatcat attaatcatc ctctttctca taaagggggt tgttttcaaa tttccttggt
     1981 tgaaaggagt taaaaaacat agatgcatca tctacaggaa caccaataaa ctctccataa
     2041 taaggatcat ctataggaaa ctcttctaat gaaacataaa acaatacatt ccagttgaag
     2101 atcattggat cactattatc tatttcatgg agcaatcttt catccttagt taattctcct
     2161 ggaattaata catcagtatg ataaaaaccg ctgtaataag aactattacc ggtgtgcact
     2221 gggcatccaa aacgatccaa tttagattct gaatgccatg ttgtagaaat cccttccgga
     2281 tgtgaatacc caccgttacc aacagactga atagtcatgt tacgaatatc cgctaacgct
     2341 tgttcttgat ctttatagaa acctttttct atcgccagcc tcataaaatg ccccggggca
     2401 tttacagaaa taagtattcc ccccggtatt cttctatcat gatttcttgt tctatgagca
     2461 gaagagtaaa aaacattaac accagcctta tatattttta gcccatcttt atcctgaaat
     2521 ggtacgcttt cagtataaat aacatcctct tttattggat agcactctgg catatgcagc
     2581 gaacaaatat atttttgtat gtccactaac tcttctgatg gacgagcaaa tgcaagttgt
     2641 ggatgaataa aataaatgag atgcgcactg acctctcctc ttcttgcgcg ttctttaaaa
     2701 cgaactcttt cattacgcaa aaaatcaaac aaatgaccat catcattata tagttggggg
     2761 ctatttacaa tagataaatg gaaatcaagc cctttaattt tcttgcttgc caatttacca
     2821 aatacacagg gctgattgcc tgacacccat tttcttagta aatcttcaat tttatcttta
     2881 gaagtttcgt taaagataaa tgaatgaata ttatcaatat cttttccaaa tgaaaaactg
     2941 gatgataatt gtggtagttt atttatacgt tgttgaagat tcatgaaagc tcccacaaga
     3001 cacctcatat attttttata tactgaaact acattatatt tattaccgac gtaaaacgaa
     3061 ataatttatt atcgttaccg atattttaaa aaatcattat ttgcacagtg ttcgagttgt
     3121 tagtatcact ccttcctgaa aatccgctcc atttaccata acgtcgcatt gtacgcaccg
     3181 ccaaaacgcg ttcggtgcga tcacggcagc agacaggtaa aaatggcaac aaaccacccg
     3241 aaaaactgcc gcgatcgcac ccgataaatt ttaaccacat gcatagctat gcagccatgt
     3301 gaatcacgca ggaattgcca gccagagact gctgaaacgg atttttttca tactttcgga
     3361 aaggcagaag acggaaccgg agcggaaaaa cagaaattca tgggaatgag cgcgatctgg
     3421 caataacggc aaaacacagc aacaaagaca caccagaatc gcgcccgcat gcgttttaac
     3481 gcgttcctgt gttttcagca agctctgact gaagcgcgtt cccggtgccc ccgaaccaac
     3541 cattatccca aaaaatgcac cggaaacgcg ctgccaacat tttagcctgt ctctggttac
     3601 catcccagcg aagggccatc cagtgtccgt tcctgaattt ccggctggcg ctcccgctcc
     3661 agggataacg catattcgcg ctcctgtatc agccgctcat cccttatctc cagttctcgc
     3721 tgtataactg gctcaagcgt tctgtccgct cgctcaagtg ctgcacctgc tgactcaact
     3781 gcatgactcg cccgttcagc atcgcgttgt cccgttgcgt aagcgaaaac attttctgca
     3841 attccacgaa ggcgttctcc cattcgttca gccgctgcat atagtcctgt tgcagttgct
     3901 ctaatgcgtt cagcaaatgt ctttccagct ccgtcatgct ctgtcactcc tgcaccagtc
     3961 tcactgcgtt cagtttgccg ttgtccttcg tccagttcgt ttcggctttc atccccttcg
     4021 gcaacaccag aaaacgtccg ttgctgtcct cgtgataacg cacgccccat gtcttcgcgt
     4081 tcagcttctc cagactctct ttctgctcgc ggagaatatt catattcgcg tttatcttca
     4141 tgccctggta ccacagcaga ctcccggtcg tggcaaacat cagtactgag acgataatca
     4201 gccacagcca gcgtttcacg ctcattttca gtacggtttt ccagtgcgcg tccatcgtat
     4261 cgacggtcgt tttctgatac ctctccagca gttctttcag ggctgttgta tggtcgttga
     4321 tagcgttcct gattaaagat tcgtttgagg tcagttccct gtttacagat tcttcgagct
     4381 tcctgaactc gtcgttcagc attttctctg tagattcggc tctctctttc agctttttct
     4441 cgaactccgc gcccgtctgt aaaagattgc tcataaaacg ctcctttcag tctgatattc
     4501 ctcccgccgt tcgggtctgc aatgctgata ctgcttcgcg tcaccctgac cacttcaagc
     4561 cccgcctctg tgagcgcctg aatcacatcc tgacggcctt ttatctctcc ggcatggtaa
     4621 agcgcgtcta tcccgcgtgt gacgccctca gcaagcgcct gtttcgtttc cggcaggtta
     4681 tcaggaaggg tcagcgtccg gcggttctcc ggggcgttgg ggtcatgcag accgtaatgg
     4741 tgattcacca gcgtctgcca ggcatcaatt ctcggcctgt ctgcccggtc gtagtacggc
     4801 tggaggcgtt ttccggtctg tagctccatg ttcggaatga caaaattcag ctcaagccgt
     4861 cccttgtcct ggtgctccac ccacaggatg ctgtactgat ttttctcgag accgggcatc
     4921 agtacacgct caaagctcgc catcactttt tcacgccctc caggcggcag ctccttctcc
     4981 gcgaacgaca gaacacctga cgtgtatttc ttcgcaaatg gcgtggcatc gatgagttcc
     5041 cggacctctt ccggattccc ctgaagcacc gttgcccctt cccggttacg ctcccttccc
     5101 agcaggtaat caaccggacc actgccacca ccttttcccc tggcatgaaa cttaactatc
     5161 atcccgcgcc ccctgttccc tgaccgccag acgcagccgg cgcagctcat ccccgatggc
     5221 tatcagtgcg gccaccacct gaacccggtc accggaagac cactgcccgc tgttcacctt
     5281 cctcgctgtc tggttaaggt tattcccgat agcggccagc tgacgcagta acggcggtgc
     5341 cagtgtcggc agcttcccgg aacgggcaac aggctcaccc aggcagaccc gccgcatcca
     5401 tgccgccagt tgtttaccct cacagcgttc cagtaaacgg gcatgctcat catcagtcac
     5461 ccgtatcgtg agcatcctct cgcgtttcat cggtatcatt acccccatga acagaaatcc
     5521 cccttacacg gaggcatcca gtgactaaac aggaaaaaac cgcccttaac atggtccgct
     5581 ttatcagaag ccagacatta acgctgctgg agaagctcaa cgaactggac gcggatgaac
     5641 aggcagacat ctgtgaatcg cttcacgacc acgccgatga gctttaccgc agttgcctcg
     5701 cacgcttcgg ggatgacggt gaaaaccgct gacacatgca gctcccggag acggtcacag
     5761 cttgtctgtg agcggatgcc gggagcagac aagcccgcca gggcgcgtca ggccgttgac
     5821 ctttggggtg tcggggcgaa gccctgaccc agtcacgtag cgatagcgga gtgt
//
